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Crystal Structure of human PMS2 N-terminal domain with AMP-PCP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EA6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.25 293 0.2 M LiCl
2.3 M Na K Phosphate pH=6.25
Crystal Properties Matthews coefficient Solvent content 2.31 46.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.104 α = 90 b = 74.572 β = 90 c = 135.885 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 X 16M 2020-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.999 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.56 50 93 0.171 0.184 8.5 8 17377
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.56 2.81 70.7 1.435 154.5 1.3 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.56 50 17377 1059 68.915 0.209 0.2077 0.2072 0.2361 0.2429 56.529
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.809 1.705 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.253 r_dihedral_angle_3_deg 11.207 r_lrange_it 6.387 r_lrange_other 6.313 r_dihedral_angle_1_deg 6.281 r_mcangle_it 3.876 r_mcangle_other 3.876 r_scangle_it 3.505 r_scangle_other 3.493 r_mcbond_it 2.202
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 11.253 r_dihedral_angle_3_deg 11.207 r_lrange_it 6.387 r_lrange_other 6.313 r_dihedral_angle_1_deg 6.281 r_mcangle_it 3.876 r_mcangle_other 3.876 r_scangle_it 3.505 r_scangle_other 3.493 r_mcbond_it 2.202 r_mcbond_other 2.202 r_scbond_it 2.042 r_scbond_other 2.014 r_angle_refined_deg 1.02 r_angle_other_deg 0.44 r_symmetry_xyhbond_nbd_refined 0.178 r_symmetry_nbd_other 0.161 r_nbd_refined 0.16 r_nbtor_refined 0.153 r_dihedral_angle_2_deg 0.14 r_nbd_other 0.114 r_symmetry_nbd_refined 0.091 r_dihedral_angle_other_2_deg 0.086 r_xyhbond_nbd_refined 0.085 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.047 r_ncsr_local_group_1 0.03 r_ext_dist_refined_b 0.007 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4666 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing